Fig. 3

RNAseq experimental setup and comparison of gene sets responsive to Pam3CSK4 or flagellin stimulation. a, setup of the RNAseq experiment. Zebrafish embryos received a 1 nl injection of 1 mg/ml Pam3CSK4 and 100 μg/ml flagellin respectively into the caudal vein at 27hpf. Control embryos were injected with water. Samples for RNAseq were taken at 1hpi. The numbers of differentially expressed genes were assessed by two criteria: 1) p < 0.01, 2 fold-change or 2) adjusted p-value <0.01, without FC cut-off. b Venn diagram showing the overlap between DEGs from Pam3CSK4 and flagellin stimulations and their GO terms annotation. c Fold-change values of inflammatory genes in RNAseq. d Filtering of 264 DEGs from Pam3CSK4 stimulation (p < 0.01, 2 fold-change) by the flagellin non-specific set (22611 genes, p > 0.05; <1.4-fold change) results in 48 Pam3CSK4 specific genes, which are grouped according to their GO terms annotation. e Filtering of 306 DEGs from flagellin stimulation (p < 0.01, 2 fold-change) by the Pam3CSK4 non-specific set (22391 genes, p > 0.05; <1.4-fold change), results in 42 flagellin specific genes, which are grouped according to their GO terms annotation. DEGs, differentially expressed genes; FC, fold-change